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| Status |
Public on Dec 31, 2019 |
| Title |
DOM_M8_P3 |
| Sample type |
SRA |
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| Source name |
Mus domesticus e17.5 placenta
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| Organism |
Mus musculus domesticus |
| Characteristics |
tissue: placenta
pregnancy type code: DOM
placenta weight (g): 0.0505
embryo weight (g): 0.6639
placenta (percent embryo weight): 7.61
embryo sex: f
# males in litter: 2
# females in litter: 2
litter size: 4
proportion males in litter: 0.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
Pregnant females (n=5/type of pregnancy) were euthanized by cervical dislocation between 10:00 and 11:00 AM on embryonic day 17-18 (e17.5) and the maternal brain was extracted. Embryos were separated from placentas and placentas were weighed, and the maternally-derived decidual layer was removed as previously described (Qu et al. 2014) and discarded. Only fetally-derived placental tissue was used in this study. All tissues were transferred immediately to RNAlater (Thermo Fisher, USA), kept at 4°C overnight to allow RNAlater perfusion, and stored at -20°C until microdissection and RNA extraction. The maternal MPoA was localized using the Mouse Brain atlas (Figs. 26-33, (Paxinos and Franklin 2013)), and microdissected by sectioning the RNAlater perfused brain at 100μm on a Leica CM 1950 cryostat, followed by dissection under a dissecting microscope in chilled PBS droplets for improved visibility of brain microstructure.
Library preparation was performed by the sequencing facility (Novogene, Sacramento, CA), using the NEB Next Ultra RNA library prep kit for Illumina.
RNAseq was performed on the Illumina HiSeq 4000 platform, producing >30 million, 150bp paired-end reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Placenta_raw_counts.txt
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| Data processing |
QC of raw sequencing reads and trimming were performed in Trim Galore! 0.4.5 (Brabraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), using a phred score cutoff of 30 and minimum sequence length of 100 after trimming.
A pseudo-hybrid (Mus domesticus X Mus spretus) genome using was generated based on the mouse genome (GRCm38.89) using the genome preparation tool of the program SNPsplit (Brabraham Bioinformatics). All placenta samples were mapped to the pseudo-hybrid genome.
Mapping was done using HISAT2 2.1
After mapping we filtered the resulting alignment files using SAMtools 0.1.19, retaining only high quality (HISAT2 MAPQ score 40), uniquely mapped, paired reads for analysis.
All alignments were randomly downsampled to ~40 million reads using SAMtools 0.1.19 to account for a possible mapping bias and to improve comparability.
Transcript quantification and annotation was done using StringTie 1.3.3. Gene annotation information was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org) for Mus spretus (SPRET/EiJ_v1.86) and Mus domesticus (WSB/EiJ_v1.86). Mouse genome annotation was used for samples mapped to the pseudo-hybrid genome (GRCm38.89). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential gene expression.
Differential expression was tested with DESeq2 1.16.1. Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt). Low counts were removed by the independent filtering process implemented in DESeq2.
Genome_build: MPA samples were mapped to WSB/EiJ_v1 for Mus domesticus and SPRET/EiJ_v1 for Mus spretus; All placenta samples were mapped to the pseudo-hybrid genome.
Supplementary_files_format_and_content: comma-separated text files include raw counts, tab-delimited supplementary text files include DEseq2 normalized counts and DESeq2 differential expression analysis outputs for each comparison
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| Submission date |
Feb 12, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Polly Campbell |
| E-mail(s) |
polly.campbell@ucr.edu
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| Organization name |
University of California Riverside
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| Department |
Evolution, Ecology, and Organismal Biology
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| Street address |
3401 Watkins Drive
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| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platform ID |
GPL26184 |
| Series (1) |
| GSE126469 |
Placental effects on maternal brain revealed by disrupted placental gene expression in mouse hybrids |
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| Relations |
| BioSample |
SAMN10922067 |
| SRA |
SRX5369911 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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